Structure of PDB 2vbv Chain B Binding Site BS02

Receptor Information
>2vbv Chain B (length=136) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDR
EFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTY
HSSEIIEIIAPMKLREQFNLKDGDVIKILIKGDKDE
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain2vbv Chain B Residue 1137 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2vbv A Ctp-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G14 G16 G18 R19 Y40 G42 T43 L44 N45 M112 K113 L114 R115
Binding residue
(residue number reindexed from 1)		G14 G16 G18 R19 Y40 G42 T43 L44 N45 M112 K113 L114 R115
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.161: CTP-dependent riboflavin kinase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0008531 riboflavin kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0009231 riboflavin biosynthetic process
GO:0009398 FMN biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vbv, PDBe:2vbv, PDBj:2vbv
PDBsum2vbv
PubMed18073108
UniProtQ60365|RIFK_METJA Riboflavin kinase (Gene Name=ribK)

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